gs2_save – GS2

FIXME : Add documentation

Uses

- mp
- constants
- netcdf_utils
- netcdf

Variables

read_many save_many include_explicit_source_in_restart proc_to_save_fields restart_file g_dim_names field_dim_names tmpr tmpi ftmpr ftmpi stmp atmp include_parameter_scan has_netcdf_parallel

Subroutines

gs2_save_for_restart gs2_save_slice gs2_restore_many gs2_save_response gs2_restore_response init_eigenfunc_file add_eigenpair_to_file finish_eigenfunc_file init_gs2_save set_restart_file finish_gs2_save deallocate_arrays restore_current_scan_parameter_value init_dt init_vnm init_ant_amp read_t0_from_restart_file

Variables

Type	Visibility	Attributes		Name		Initial
logical,	public		::	read_many	=	.false.	Read and write single or multiple restart files. Effectively ignored if not built with parallel netcdf
logical,	public		::	save_many	=	.false.	Read and write single or multiple restart files. Effectively ignored if not built with parallel netcdf
logical,	public		::	include_explicit_source_in_restart	=	.true.	Do we want to include the explicit source terms and related timesteps when saving/restoring from the restart file.
integer,	public		::	proc_to_save_fields			Which processor should save the potentials. If <0 (default) then all processors save their potentials. If >= nproc then will be set to mod(proc_to_save_fields, nproc)
character(len=run_name_size),	private		::	restart_file			Used to hold the base of the restart file name.
character(len=5),	private,	parameter, dimension(*)	::	g_dim_names	=	["theta", "sign ", "glo "]	Names of dimensions for distribution-sized variables in netCDF files
character(len=5),	private,	parameter, dimension(*)	::	field_dim_names	=	["theta", "akx ", "aky "]
real,	private,	allocatable, dimension(:,:,:)	::	tmpr
real,	private,	allocatable, dimension(:,:,:)	::	tmpi
real,	private,	allocatable, dimension(:,:,:)	::	ftmpr
real,	private,	allocatable, dimension(:,:,:)	::	ftmpi
real,	private,	allocatable, dimension(:)	::	stmp
real,	private,	allocatable, dimension(:)	::	atmp
logical,	private,	parameter	::	include_parameter_scan	=	.true.	Do we save the scan parameter or not?
logical,	private,	parameter	::	has_netcdf_parallel	=	.false.	The NETCDF_PARALLEL directives include code for parallel netcdf using HDF5 to write the output to a single restart file The save_many/read_many flag allows the old style multiple file output Here we set a run time flag to enable us to handle some of the different paths through the code at run time rather than with ifdef mazes

Interfaces

public interface gs2_restore

private subroutine gs2_restore_many(g, scale, istatus, has_phi, has_apar, has_bpar, fileopt)

FIXME : Add documentation

Arguments

Type	Intent	Optional	Attributes		Name
complex,	intent(out),		dimension (-ntgrid:,:,g_lo%llim_proc:)	::	g
real,	intent(in)			::	scale
integer,	intent(out)			::	istatus
logical,	intent(in)			::	has_phi
logical,	intent(in)			::	has_apar
logical,	intent(in)			::	has_bpar
character(len=*),	intent(in),	optional		::	fileopt

Derived Types

type, public :: EigNetcdfID

A custom type to look after the netcdf ids for the eigenvalue file

Components

Type	Visibility	Attributes		Name		Initial
integer,	public		::	ncid			File handle
integer,	public		::	nconv_count			Current size of `conv` dimension

Functions

public function restart_writable(read_only, my_file, error_message)

This function checks to see if we can create a file with name // if not then our restarts are not going to be possible and we return false. Can also be used to check that we can read from the restart file (which assumes it exists).

Arguments

Type	Intent	Optional	Attributes		Name
logical,	intent(in),	optional		::	read_only	If present and true, only check that files can be read
character(len=*),	intent(in),	optional		::	my_file	An optional specific filename to check
character(len=:),	intent(out),	optional,	allocatable	::	error_message	Error message returned from `open` if there was a problem

Return Value logical

private function get_file_proc(is_one_file_per_processor, fileopt) result(file_proc)

Returns the file corresponding to restart file in current setup

Arguments

Type	Intent	Optional	Attributes		Name
logical,	intent(in)			::	is_one_file_per_processor
character(len=*),	intent(in),	optional		::	fileopt

Return Value character(len=run_name_size)

Subroutines

public subroutine gs2_save_for_restart(g, t0, vnm, has_phi, has_apar, has_bpar, code_dt, code_dt_prev1, code_dt_prev2, code_dt_max, fileopt, save_glo_info_and_grids, save_velocities, header)

Create and fill the restart files

Arguments

Type	Intent	Optional	Attributes		Name
complex,	intent(in),		dimension (-ntgrid:,:,g_lo%llim_proc:)	::	g	The distribution function $g$
real,	intent(in)			::	t0	Current simulation time
real,	intent(in),		dimension (2)	::	vnm	FIXME: Collisionality multiplier?
logical,	intent(in)			::	has_phi	Do we include electrostatic potential, $\phi$
logical,	intent(in)			::	has_apar	Do we include vector potential, $A_\parallel$
logical,	intent(in)			::	has_bpar	Do we include parallel magnetic field, $B_\parallel$
real,	intent(in)			::	code_dt	The current time step, the two previous time steps and the maximum allowed time step.
real,	intent(in)			::	code_dt_prev1	The current time step, the two previous time steps and the maximum allowed time step.
real,	intent(in)			::	code_dt_prev2	The current time step, the two previous time steps and the maximum allowed time step.
real,	intent(in)			::	code_dt_max	The current time step, the two previous time steps and the maximum allowed time step.
character(len=*),	intent(in),	optional		::	fileopt	Optional extra filename infix
logical,	intent(in),	optional		::	save_glo_info_and_grids	Control if layout and diagnostic information is saved
logical,	intent(in),	optional		::	save_velocities	Control if $v_\parallel, v_\perp$ information is saved
type(standard_header_type),	intent(in),	optional		::	header	Header for files with build and run information

public subroutine gs2_save_slice(g_in, it, ik, il, ie, is, time, nout, fileopt, header)

Save g slices

Arguments

Type	Intent	Optional	Attributes		Name
complex,	intent(in),		dimension (-ntgrid:, :, g_lo%llim_proc:)	::	g_in	The distribution function $g$
integer,	intent(in)			::	it	The indices of the slice to save
integer,	intent(in)			::	ik	The indices of the slice to save
integer,	intent(in)			::	il	The indices of the slice to save
integer,	intent(in)			::	ie	The indices of the slice to save
integer,	intent(in)			::	is	The indices of the slice to save
real,	intent(in)			::	time	The current time
integer,	intent(in),	optional		::	nout	The current time output index
character(len=*),	intent(in),	optional		::	fileopt	Optional extra filename infix
type(standard_header_type),	intent(in),	optional		::	header	Header for files with build and run information

private subroutine gs2_restore_many(g, scale, istatus, has_phi, has_apar, has_bpar, fileopt)

FIXME : Add documentation

Arguments

Type	Intent	Optional	Attributes		Name
complex,	intent(out),		dimension (-ntgrid:,:,g_lo%llim_proc:)	::	g
real,	intent(in)			::	scale
integer,	intent(out)			::	istatus
logical,	intent(in)			::	has_phi
logical,	intent(in)			::	has_apar
logical,	intent(in)			::	has_bpar
character(len=*),	intent(in),	optional		::	fileopt

public subroutine gs2_save_response(resp, fname, code_dt, condition, header)

This routine writes a passed square complex array to a file with passed name

Arguments

Type	Intent	Optional	Attributes		Name
complex,	intent(in),		dimension(:,:)	::	resp
character(len=*),	intent(in)			::	fname
real,	intent(in)			::	code_dt
real,	intent(in),	optional		::	condition
type(standard_header_type),	intent(in),	optional		::	header	Header for files with build and run information

public subroutine gs2_restore_response(resp, fname, code_dt, condition)

This routine reads a square complex array from a file with passed name

Arguments

Type	Intent	Optional	Attributes		Name
complex,	intent(out),		dimension(:,:)	::	resp
character(len=*),	intent(in)			::	fname
real,	intent(out)			::	code_dt
real,	intent(out),	optional		::	condition

public subroutine init_eigenfunc_file(fname, IDs)

Initialises a file for saving output of eigensolver to netcdf

Arguments

Type	Intent	Optional	Attributes		Name
character(len=*),	intent(in)			::	fname
type(EigNetcdfID),	intent(inout)			::	IDs

public subroutine add_eigenpair_to_file(eval, has_phi, has_apar, has_bpar, IDs, my_conv)

Add an eigenpairs data to file

Arguments

Type	Intent	Optional		Name
complex,	intent(in)		::	eval
logical,	intent(in)		::	has_phi
logical,	intent(in)		::	has_apar
logical,	intent(in)		::	has_bpar
type(EigNetcdfID),	intent(inout)		::	IDs
real,	intent(in),	optional	::	my_conv

public subroutine finish_eigenfunc_file(IDs)

Close the eigenfunction file

Arguments

Type	Intent	Optional	Attributes		Name
type(EigNetcdfID),	intent(inout)			::	IDs

public subroutine init_gs2_save()

FIXME : Add documentation

Arguments

None

public subroutine set_restart_file(file)

Sets the base of the restart file to be used when writing/reading files.

Arguments

Type	Intent	Optional	Attributes		Name
character(len=*),	intent(in)			::	file

public subroutine finish_gs2_save()

FIXME : Add documentation

Arguments

None

private subroutine deallocate_arrays()

Deallocate all module level arrays

Arguments

None

public subroutine restore_current_scan_parameter_value(current_scan_parameter_value)

FIXME : Add documentation

Arguments

Type	Intent	Optional	Attributes		Name
real,	intent(out)			::	current_scan_parameter_value

public subroutine init_dt(delt0, delt1, delt2, delt_max, istatus, not_set_value)

FIXME : Add documentation

Arguments

Type	Intent	Optional		Name
real,	intent(inout)		::	delt0
real,	intent(inout)		::	delt1
real,	intent(inout)		::	delt2
real,	intent(inout)		::	delt_max
integer,	intent(out)		::	istatus
real,	intent(in),	optional	::	not_set_value

public subroutine init_vnm(vnm, istatus)

FIXME : Add documentation

Arguments

Type	Intent	Optional	Attributes		Name
real,	intent(inout),		dimension(2)	::	vnm
integer,	intent(out)			::	istatus

public subroutine init_ant_amp(a_ant, b_ant, nk_stir, istatus)

FIXME : Add documentation

Arguments

Type	Intent	Attributes		Name
complex,	intent(inout),	dimension(:)	::	a_ant
complex,	intent(inout),	dimension(:)	::	b_ant
integer,	intent(in)		::	nk_stir
integer,	intent(out)		::	istatus

public subroutine read_t0_from_restart_file(tstart, istatus)

FIXME : Add documentation

Arguments

Type	Intent	Optional	Attributes		Name
real,	intent(inout)			::	tstart
integer,	intent(out)			::	istatus

gs2_save Module

Contents

Uses

Contents

Variables

Interfaces

public interface gs2_restore

private subroutine gs2_restore_many(g, scale, istatus, has_phi, has_apar, has_bpar, fileopt)

Arguments

Derived Types

type, public :: EigNetcdfID

Components

Functions

public function restart_writable(read_only, my_file, error_message)

Arguments

Return Value logical

private function get_file_proc(is_one_file_per_processor, fileopt) result(file_proc)

Arguments

Return Value character(len=run_name_size)

Subroutines

public subroutine gs2_save_for_restart(g, t0, vnm, has_phi, has_apar, has_bpar, code_dt, code_dt_prev1, code_dt_prev2, code_dt_max, fileopt, save_glo_info_and_grids, save_velocities, header)

Arguments

public subroutine gs2_save_slice(g_in, it, ik, il, ie, is, time, nout, fileopt, header)

Arguments

private subroutine gs2_restore_many(g, scale, istatus, has_phi, has_apar, has_bpar, fileopt)

Arguments

public subroutine gs2_save_response(resp, fname, code_dt, condition, header)

Arguments

public subroutine gs2_restore_response(resp, fname, code_dt, condition)

Arguments

public subroutine init_eigenfunc_file(fname, IDs)

Arguments

public subroutine add_eigenpair_to_file(eval, has_phi, has_apar, has_bpar, IDs, my_conv)

Arguments

public subroutine finish_eigenfunc_file(IDs)

Arguments

public subroutine init_gs2_save()

Arguments

public subroutine set_restart_file(file)

Arguments

public subroutine finish_gs2_save()

Arguments

private subroutine deallocate_arrays()

Arguments

public subroutine restore_current_scan_parameter_value(current_scan_parameter_value)

Arguments

public subroutine init_dt(delt0, delt1, delt2, delt_max, istatus, not_set_value)

Arguments

public subroutine init_vnm(vnm, istatus)

Arguments

public subroutine init_ant_amp(a_ant, b_ant, nk_stir, istatus)

Arguments

public subroutine read_t0_from_restart_file(tstart, istatus)

Arguments